RetrogeneDB ID: retro_lafr_73

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:47386878..47387418(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030504
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSLAFG00000003164
• Aliases: None
• Description: None

Sequence

>retro_lafr_73
ATGGCTTCCCAGAACCACGACCCAGCCGCAGCCAGCGTTGTCGCCGCCCAGAAAGGGACTGAGCCCAGCGGAGGCGCCGC
CCGGGGCTCCGTGGGCAAGAGGCTACAGCAGGAGTTGATGACCCTCATGATGTCTGGTGACAAAGGAATTTCTGCCTTCC
CTGAATCAGACAACCTTTTCAAGTGGGTGGGGACCATCCATGGAGCAGCTGGCACAGTATATGAAGACCTGAGGTGTAAG
CTCTCTCTCGAGTTCCCCAGTGGCTACACTTACAATGCGCCCACGGTGAAGTTCCTCACGCCCTGCTACCACCCCAGCGT
GGACACTCAGGGTAACATCTGCCTAGACATCCTGAAGGACAAGTGGTCTGCCCTGTACGATGTCAGGACCATCCTCCTCT
CTATCCAGAGCCTGCTGGGAGAACCCAACATCGATAGCCCCTTAAACACACATGCTGCCGAGCTCTGGAAAAACCCCACA
GCCTTTAAGAAGTACCTGCAGGAAACCTACTCAAAGCAAGTCTCCAGCCAAGAGCCCTGA

Alignment

ORF - retro_lafr_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQNRDPAAASVVAARKGTEPSGGAARGSVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
          MASQN.DPAAASVVAA.KGTEPSGGAARGSVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
Retrocopy MASQNHDPAAASVVAAQKGTEPSGGAARGSVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA

Parental  GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKDKWSALYDVRTILLSIQSLLG
          GTVYEDLR.KLSLEFPSGY.YNAPTVKFLTPCYHP.VDTQGNICLDILKDKWSALYDVRTILLSIQSLLG
Retrocopy GTVYEDLRCKLSLEFPSGYTYNAPTVKFLTPCYHPSVDTQGNICLDILKDKWSALYDVRTILLSIQSLLG

Parental  ATEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVSSQEP
          ..EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVSSQEP
Retrocopy --EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVSSQEP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_73 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012547	5 retrocopies	retro_amel_1122, retro_amel_1353, retro_amel_157, retro_amel_1621, retro_amel_635,
Bos taurus	ENSBTAG00000016746	1 retrocopy	retro_btau_249,
Canis familiaris	ENSCAFG00000009745	6 retrocopies	retro_cfam_1031, retro_cfam_1805, retro_cfam_1878, retro_cfam_2078, retro_cfam_290, retro_cfam_356,
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902,
Equus caballus	ENSECAG00000014619	2 retrocopies	retro_ecab_297, retro_ecab_316,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Echinops telfairi	ENSETEG00000012346	18 retrocopies	retro_etel_1212, retro_etel_1500, retro_etel_1560, retro_etel_157, retro_etel_1634, retro_etel_1729, retro_etel_1853, retro_etel_1856, retro_etel_2013, retro_etel_221, retro_etel_321, retro_etel_324, retro_etel_400, retro_etel_628, retro_etel_689, retro_etel_764, retro_etel_824, retro_etel_909,
Felis catus	ENSFCAG00000001885	4 retrocopies	retro_fcat_1440, retro_fcat_1530, retro_fcat_1667, retro_fcat_1734,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73 ,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Microcebus murinus	ENSMICG00000011218	2 retrocopies	retro_mmur_332, retro_mmur_988,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Sarcophilus harrisii	ENSSHAG00000002117	1 retrocopy	retro_shar_832,
Sus scrofa	ENSSSCG00000007423	1 retrocopy	retro_sscr_643,